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Layout genomes

Source: R/gggenomes.R
layout_genomes.Rd

Layout genomes

Usage

layout_genomes(
  seqs = NULL,
  genes = NULL,
  feats = NULL,
  links = NULL,
  infer_bin_id = seq_id,
  infer_start = min(start, end),
  infer_end = max(start, end),
  infer_length = max(start, end),
  adjacent_only = TRUE,
  marginal = "drop",
  ...
)

Arguments

seqs

A data.frame or a character vector with paths to files containing sequence data. Data columns:

  • required: seq_id,length

  • recognized: bin_id,start,end,strand

genes, feats

A data.frame, a list of data.frames, or a character vector with paths to files containing gene data. Each item is added as feature track.

For a single data.frame the track_id will be "genes" and "feats", respectively. For a list, track_ids are parsed from the list names, or if names are missing from the name of the variable containing each data.frame. Data columns:

  • required: seq_id,start,end

  • recognized: strand,bin_id,feat_id,introns

A data.frame or a character vector with paths to files containing link data. Each item is added as links track. Data columns:

  • required: seq_id,seq_id2

  • recognized: start,end,bin_id,start2,end2,bin_id2,strand

infer_length, infer_start, infer_end, infer_bin_id

used to infer pseudo seqs if only feats or links are provided, or if no bin_id column was provided. The expressions are evaluated in the context of the first feat or link track.

By default subregions of sequences from the first to the last feat/link are generated. Set infer_start to 0 to show all sequences from their true beginning.

adjacent_only

Indicates whether links should be created between adjacent sequences/chromosomes only. By default it is set to TRUE. If set to FALSE, links will be created between all sequences. This is not recommended for large data sets as it slow and plots become way to cluttered to be legible.

marginal

How to handle feats/genes and links overlapping edges of sequence regions when providing sequence start/end or after zooming in with focus(). Choices are to "drop", "keep" or "trim", with "drop" as the default. You can provide two values to specify different behavior for feats/genes and links. See vignette("marginal", package = "gggenomes") for more details.

...

additional parameters, passed to layout

Value

gggenomes_layout object